[gmx-users] Regarding em potential energy coming possitive

[Swagata Patra]

Thank you Justin.

On Thu, Sep 29, 2016 at 6:37 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 9/28/16 9:03 PM, Swagata Patra wrote:
>
>> Thank you so much for clarifying my doubt.
>>
>> But why potential energy coming so high? Is it because Fmax<1?
>>
>>
> There's nothing abnormal about your potential energy.  It's also not
> "high" because it's a negative number, exactly in the range where you would
> expect an average-sized, solvated protein system.
>
>
> -Justin
>
> On Thu, Sep 29, 2016 at 6:29 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 9/28/16 8:57 PM, Swagata Patra wrote:
>>>
>>> Thank you Justin for your reply.
>>>> So is it required to do more round of EM or should i proceed to NVT
>>>> step?
>>>>
>>>>
>>>> If this is just normal MD, yes.  There's no need to try to get Fmax < 1
>>> for that.
>>>
>>> -Justin
>>>
>>>
>>> On Thu, Sep 29, 2016 at 6:23 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>
>>>>
>>>>
>>>>
>>>>> On 9/28/16 8:50 PM, Swagata Patra wrote:
>>>>>
>>>>> Hello everyone,
>>>>>
>>>>>>
>>>>>> I am facing a problem in energy minimization step. I am not sure if
>>>>>> the
>>>>>> system is energy minimized or not. After completing the em, I am
>>>>>> getting
>>>>>> the following message:
>>>>>> Reached the maximum number of steps before reaching Fmax < 1
>>>>>>
>>>>>> Steepest Descents did not converge to Fmax < 1 in 100001 steps.
>>>>>> Potential Energy  = -9.38185842721980e+06
>>>>>> Maximum force     =  4.73530543550372e+02 on atom 1694
>>>>>> Norm of force     =  1.11096437377417e+00
>>>>>> But when I am calculating the potential energy getting the following
>>>>>> message:
>>>>>> Energy                      Average   Err.Est.       RMSD  Tot-Drift
>>>>>> ------------------------------------------------------------
>>>>>> -------------------
>>>>>> Potential                   121.811    1.9e+06        nan   -2017.89
>>>>>>  (kJ/mol)
>>>>>>
>>>>>> Potential energy should come negative. But here its too high.
>>>>>> One more thing that I want to tell is, in my protein pdb file there is
>>>>>> gap
>>>>>> between amino acids(like G229 then H412). That's why in topology file
>>>>>> I
>>>>>> am
>>>>>> getting two chains.
>>>>>> Please suggest me what could be the problem?
>>>>>>
>>>>>>
>>>>>> I don't see a problem.  The energy is fine and the maximum force is
>>>>>> fine
>>>>>>
>>>>> for most purposes.  You only need to achieve Fmax < 1 for NMA, but to
>>>>> do
>>>>> so
>>>>> you probably need a few rounds of EM, not just a single run of steepest
>>>>> descents.
>>>>>
>>>>> -Justin
>>>>>
>>>>> --
>>>>> ==================================================
>>>>>
>>>>> Justin A. Lemkul, Ph.D.
>>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>>>
>>>>> Department of Pharmaceutical Sciences
>>>>> School of Pharmacy
>>>>> Health Sciences Facility II, Room 629
>>>>> University of Maryland, Baltimore
>>>>> 20 Penn St.
>>>>> Baltimore, MD 21201
>>>>>
>>>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>>>> http://mackerell.umaryland.edu/~jalemkul
>>>>>
>>>>> ==================================================
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>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 629
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
>>> ==================================================
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>>>
>>
>>
>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
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> Gromacs Users mailing list
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-- 
Swagata Patra
M.Tech (Biotech)
JRF
IIT Guwahati